It is actually through a system call in Matlab. I've nearly finished a process to support stdin/stdout back and forth communication but I need some results ASAP and all I was getting was flashing screens as a new window would pop up and close.
start /B /WAIT and now it seems to be working exactly as desired.
Thanks for the note on the parallel computation approach, although I don't have that many simulations to run yet and I need a bit of back and forth communication for everything to work.
This is an extension of this topic from a while back, although I've changed a few things since then:https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=996